This online tutorial is designed to help the first time ARDB user. This tutorial will teach you to use various ARDB
tools to search for specific information, to annotate a single gene or a whole bacteria genome, etc.
And this tutorial will also give a brief description of how to examine the results.
Generally this tutorial is partitioned into:
After this tutorial you will learn how to:
- search for specific information, such as resistance gene, type, organism or genome.
- annotate a potential resistance gene, or all the genes of a bacterial genome.
- identify mutations of a gene, whose mutations of specific positions will result in resistance.
There are two general ways to search the ARDB database, one is search by entering your keyword and the other is
by selecting various options.
Search by keyword
For convenience, this function is available at the top of every ARDB webpage.
ARDB information is organized into different categories, so
before entering your keyword, you should choose a database containing the information you need.
For example, I am interested in all the resistance genes that are resistant to tetracycline.
Then the information you need is resistance gene, and the keyword is tetracycline.
What you can do to search this specific information is first to choose "Resistance Gene" database, and
input your keyword "tetracycline".
This list below shows you how to choose appropriate database according to the information you need.
- Resistance Type
- Antibiotic resistance genes can be grouped by their resistance type. Genes belonging to the same
resistance type confer same resistance profile and have same action mechanism. This database contains information,
such as resistance profile, mechanism, requirement, epidemiology for each type.
- Resistance Gene
- Resistance gene can confer antibiotic resistance to one or several antibiotics, by inactivation,
protection, substitution, efflux pumping, etc. This database contains information, such as resistance
profile, resistance type, requirement, protein and DNA sequence for each specific gene.
This database only includes NON-REDUNDANT, NON-VECTOR, COMPLETE-SEQUENCE genes.
- Antibiotic can inhibit bacteria growth or kill them, by inhibiting cell wall synthesis, protein synthesis,
DNA synthesis and transcription, etc. This database contains information, such as action mechanism, target, synonyms
and resistance type, for each antibiotic.
- Resistance Gene(ALL)
- This database contains the same information as Resistance Gene. However it includes all genes including
REDUNDANT, VECTOR AND INCOMPLETE-SEQUENCE ones.
- Resistance Species
- This database contains resistance profile and corresponding resistance genes for each species.
- Resistance Genus
- This database contains resistance types information for each genus. In other words, what kind (type, instead of
specific genes) of resistance genes are found in a genus.
Search by Selection
This function is in the webpage of "ADVANED SEARCH". The underlining principles of this function is extactly the same as
"Search by keyword", and the difference is selecting search criteria instead of entering the keyword. At first step, choose a
database that meets your need as in "Search by keyword". Then instead of entering the keyword, you have to choose the
search word in step 2.
This section will teach you how to annotate a single potential antibiotic resistance gene or multiple genes
of a bacterial genome using BLAST.
Single Gene Annotation
Suppose you have a DNA sequence or a protein sequence of a gene, and you want to know if the DNA sequence
or protein sequence is an antibiotic resistance gene, then you can BLAST agaist the whole ARDB sequence
database to see if it has high similarity with existing identified antibiotic resistance genes. There are
several function tools to use. If you want to BLAST against all the resistance genes protein sequences, then you
can use this protein BLAST server. If you want to
BLAST against all the resistance genes DNA sequences, then you can use this DNA BLAST server. And if you want to BLAST against all the PSSMs (one for each type), you can use this RPS BLAST server.
Multiple Genes Annotation
Suppose you have a newly sequenced bacteria genome or multiple gene sequences, and you want to know if
there are antibiotic resistance gene among them. Instead of annotating them one by one as in the single
gene annotation step, you can annotate them all in once using
genome annotation server.
Aquired resistance genes (horizontal gene transfer) among bacterial strains or species are often considered to be the main mediator of
antibiotic resistance. However mutational resistance is another important way to confer resistance to particular antibiotics
(such as fluoroquinolones and oxazolidinones), especially in certain species, such as Mycobacterium tuberculosis and
Helicobacter pylori. In order to help identify the mutation resistance, relevant information are collected for 12 well studied
genes: 16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, folP, dfr. This tool maps the query sequence onto the
reference resistance gene and tries to find the specific mutations that will contribute to antibiotic resistance.
This tool allows the user to compare the resistance profile (all predicted antibiotic resistance genes) of pre-annotated genomes
and your uploaded genome.
Resistance Profiles Comparison of Pre-annotated Genomes
Suppose the user is working on the pathogenesis of Staphylococcus species, and wants to compare the antibiotic resistance profiles
of already sequenced Staphylococcus species, this is the right tool to do this job. The interface is pretty straight forward (see
below picture). First, choose the genomes you want to compare and add them to the right list, then click the "Compare" button.
You can also delete genomes from the right list.
Resistance Profiles Comparison of Uploaded Genome with other Pre-annotated Genomes
Suppose the user has a newly sequenced genome of Staphylococcus species, and wants to know the resistance profile of this genome.
At the same time, the user also wants to compare the resistance profile of this newly sequenced genome with that of other species.
This tool will help the user to do all these jobs.